reportCellQC: Get runCellQC .html report

In singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Description

A function to generate .html Rmarkdown report containing the visualizations of the runCellQC function output

Usage

reportCellQC(
  inSCE,
  output_file = NULL,
  output_dir = NULL,
  subTitle = NULL,
  studyDesign = NULL
)

Arguments

inSCE	A SingleCellExperiment object containing the filtered count matrix with the output from runCellQC function
output_file	name of the generated file. If NULL/default then the output file name will be based on the name of the Rmarkdown template.
output_dir	name of the output directory to save the rendered file. If NULL/default the file is stored to the current working directory
subTitle	subtitle of the QC HTML report. Default is NULL.
studyDesign	description of the data set and experiment design. It would be shown at the top of QC HTML report. Default is NULL.

Value

.html file

Examples

data(scExample, package = "singleCellTK")
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
## Not run: 
sce <- runCellQC(sce)
reportCellQC(inSCE = sce)

## End(Not run)

singleCellTK documentation built on Nov. 8, 2020, 5:21 p.m.